amplicR | R Documentation |
An R package to process amplicon data.
This package has a number of functions to filter, dereplicate and error and chimera check NGS reads stored in fastq files. This funcitonality is currently limted to single-read analysis. The retained reads after the data processing described above (or your own reads if you have done this already in another way) can then be compared against reference sequences and the number of mismatch is reported. This may be useful when, for example, screening samples for particular taxa (e.g. a pathogen).
amplicR
is mainly a wrapper of several functions provided by other R
packages in order to automate some common analyses, so if you use it, please
make sure to also cite the relevant packages (these are generally indicated
in the documentation of amplicR
's functions). To find out the correct
citation for a package, you can use the function:
citation("package_name")
where you have to replace package_name with
the actual name of the package you are interested into.
Use help(package = "amplicR")
for a list of
amplicR
functions and their specific documentations.
A more detailed description of the package and functions can be opened with:
vignette(package="amplicR", topic="amplicR-package")
- This is pending... hang in there
If you use amplicR
, please cite:
This is also pending
Please, use
https://github.com/carlopacioni/amplicR/issues to report any issues
with amplicR
. If unsure, or for feedback, contact me at:
carlo.pacioni 'at' gmail.com.
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